This paper describes the development of another ChIPSeq methodology, and evaluated its usefulness by creating genome- wide maps of chromatin states that distinguished three mouse cell types: embryonic stem (ES) cells, neural progenitor cells, and embryonic fibroblasts. For each group, they used ChIP to analyze the occupancy of trimethylated histones (H3K9, H3K4, H3K27, H3K36, and H4K20) and RNA polymerase II. Later, Solexa/Illumina sequencings were performed from nanogram quantities of ChIP DNAs, and reads were computationally assembled. Validation of the methodology was both by computational analysis and by comparison to other wet lab methods. This first large- scale application of pyrosequencing in epigenetics suggests that we are getting closer to the era of disease- specific epigenomic maps, and public annotated databases of chromatin- states as well.
Mikkelsen TS. et al. 2007. Nature 448: 553-560
epigenetics
More comments can be found on the same issue of Nature [Editor's summary: Chromatin profiling; and Genomic biology].
